NMRFx Processor ChangeLog

Version 10.2.18 Released 28 Aug 2018

BUG GUI Fix grid when converting overlayed window to a grid window. Wasn't retaining the dataset dims. For example, if spectra in single window had dim 1 on x and dim 3 on y, the overlay would have dim1 on x and dim 2 ony

Version 10.2.16 Released 08 Aug 2018

NEW GUI Add normalization and controls to peak graph. Useful for displaying meaasured peaks from releaxation experiments where one typically normalizes the values by dividing by the first point, and possibly also by taking the log of the normalized value (as in CPMG experiments).

NEW GUI Update to 10.2.15

BUG GUI When making simulated peak list name from dataset remove the ".nv" Peaklist names shouldn't have a "." in them. Peak lists with "." characters can be problematic when the code is figuring out the list name and peak number from a specifier like noesy.3.

NEW GUI Don't add Simulate tab in processor (only useful in Analyst)

NEW GUI Change Peak Tool to use a single Peak Navigator for Peak and Graph tabs. The two navigator controls could be out of sync with each other.

Version 10.2.10 Released 11 Nov 1986

NEW CMD Initial addition of script generator and auto execution from command line. Use via "auto" subcommand. This allows generating a processing script from the command line. The processed script can be executed immediately or just saved to a file.

NEW CMD Add new command-line scripting methods for creating a dataset, creating a dataset with fewer dimensions than original dataset, and getting a vector from dataset.

BUG CMD The DPHASE command should not auto-phase dimensions (when using dim=0 arg) if they are not frequency mode.

Version 10.2.6 Released 14 May 2018

IMPROVE GUI Allow displaying peaks where the labels don't agree, but the nuclei do

NEW GUI Add support for reading .xpk and sparky .save files

Version 10.2.4 Released 10 Apr 2018

IMPROVE CMD Allow using sf,sw pars from nmrPipe file.

IMPROVE CMD Add nusfile support to NMRPipeData

IMPROVE CMD Set Group Delay on vectors from nmrPipe file and fix sw/sf/ref

Version 10.2.2 Released 27 Mar 2018

BUG CMD BCSINE was using old style parameters Was failing because it was calling the Java code with too many args

IMPROVE CMD Improvements in baseline correction In window methods now make the window a little wider to encompass regions on each side of detected signal regions (as they may not qualify as signal regions, but still have elevated intensities that shouldn't be considered baseline. Add cwtdf in which you specify the fraction of spectrum that should be baseline.

BUG CMD Clear annotation data in VecRef op. Makes sure that apodization is no longer displayed in GUI when you remove the apodization op.

BUG CMD Sample schedule wan't being recreated when number of points changed. Caused by renaming some variables in earlier commit.

IMPROVE CMD NESTANMR now returns silently if no schedule present. Useful in doing demo in GUI when we turn schedule on/off

IMPROVE CMD Allow complex vectors to be bucketed and use method in Vec for op code

IMPROVE CMD tdSize should get set in VecRef. Windows were not getting calculated properly in demo modes because tdSize wasn't changing when vector size was changed

IMPROVE CMD Add offset arg to Blackman and Kaiser.

IMPROVE GUI Allow peak navigator to zoom to specified width around peak. Adds choice box with set of scales

BUG GUI Fix getting rows/cols of spectra. Was calculating rather than existing. .yaml file was not getting correct grid values.

IMPROVE GUI First addition of a Reference Menu. Currently only has an entry for adjusting reference of experiments with diagonal so the diagonal has same shift for each of the two dimensions.

IMPROVE GUI Add ability to freeze/thaw all peaks regardless of condition. Holding down Alt key while clicking freeze or thaw will apply to all linkded dimensions even if they are in a peak list with condition different than selected peak. Also Tweak/Freeze applys to peaks that are linked in all dimensions to the selected peak.

IMPROVE GUI Add ability to freeze/thaw all peaks regardless of condition. Holding down Alt key while clicking freeze or thaw will apply to all linkded dimensions even if they are in a peak list with condition different than selected peak. Also Tweak/Freeze applys to peaks that are linked in all dimensions to the selected peak.

Version 10.1.23 Released 11 Mar 2018

IMPROVE CMD Change Kaiser and Blackman apod to work on single, specified dim . In matrix mode, these windows were applying the apodization to all dimensions of the extracted matrices. Now they apply to a specified dimension, allowing different parameters and windows for each dim.

IMPROVE CMD Locating position of dataset maxima now uses extreme rather than max. This allows searching for plane with negative intensity in the GUIs max plane menu item.

IMPROVE CMD Allow Blackman to work as matrix op

NEW CMD Add mkinst.sh script for packaging simple .tar package with Java Useful for a distribution where you just want to unpack tar file and not use any GUI.

NEW CMD Add toPipe method to dscript.py

NEW CMD Set dataset header temperature field when processing

NEW CMD Store temperature in NMRViewJ format file header

NEW CMD Add changes for exporting a Dataset in nmrPipe format

IMPROVE CMD Add threshold to NESTA.

IMPROVE CMD Allow Kaiser window to work on matrices. This allows its use prior to nD NUS operations so each one doesn't need to support apodization.

NEW GUI Add Kaiser and BLACKMAN apodization windows as operations in operation menu

IMPROVE GUI Allow moving cross hair with meta-key down. Add checkbox for slice1. In selector mode you can now move crosshairs by dragging mouse with the meta-key . Cleaned up slice controls

IMPROVE GUI Allow dragging out a region on spectrum in selector mode. With shift down it selects peaks. With alt down it expands to selected region.

NEW GUI Add Dataset List with drag/drop and move Attributes to a popover. The Open button is replaced by a Dataset button which shows a list of currently open datasets. They can be dragged onto spectra. The attributes button now shows the Spectrum Attributes in a popover. The popover can be detached so it stays around like old one. When not detached there toolbar is not shown.

IMPROVE GUI Add a slice for second crosshair and make the slice colors (optionally) that of dataset.

NEW GUI Add Peak Selector to Spectrum Attributes dialog to allow specifying what peak list(s) is to be displayed.

NEW GUI Add simulate peak tab and code to call python methods

IMPROVE CMD Add read/write of frozen and color to peak .xpk2 files

IMPROVE GUI More work on Project. Keep list of open projects and a ref to active project. Provide getter to get active project

IMPROVE GUI Always write .mpk2 file when writing .xpk2 file

IMPROVE CMD When saving peak lists to project delete files that already exist, but don't have a peak list in memory

NEW CMD Add ability to store a list of values in Dataset and save them to .par file. Useful for relaxation delays etc.

Version 10.1.20 Released 15 Dec 2017

NEW GUI Add button for linking peaks in slider and activate/deactivate buttons based on number of peaks selected

NEW GUI Draw lines between linked peaks when slider active

IMPROVE GUI Add menu item for PeakLinker

Version 10.1.19 Released 07 Dec 2017

NEW GUI Add ability to specify a search pattern in textfield of peak navigator

NEW GUI Initial add of peak navigator to bottom bar of chart window

NEW GUI Add aa and as keyboard bindings for peak add. Fix update of dataset name in peak reference inspector

NEW GUI Add Peak Reference tab

NEW GUI Implement PeakListener in PolyChart so the peaks move in response to changes in values.